Most heritable surnames, like Y chromosomes, are passed from father to son. These unique cultural markers of coancestry might therefore have a genetic correlate in shared Y chromosome types among men sharing surnames, although the link could be affected by mutation, multiple foundation for names, nonpaternity, and genetic drift. Here, we demonstrate through an analysis of 1678 Y-chromosomal haplotypes within 40 British surnames a remarkably high degree of coancestry that generally increases as surnames become rarer. On average, the proportion of haplotypes lying within descent clusters is 62%, but ranges from zero to 87%. The shallow time-depth of many descent clusters within names, the lack of a detectable effect of surname derivation on diversity, and simulations of surname descent suggest that genetic drift through variation in reproductive success is important in structuring haplotype diversity. Modern patterns therefore provide little reliable information about the original founders of surnames some 700 years ago. A comparative analysis of published data on Y diversity within Irish surnames demonstrates a relative lack of surname frequency dependence of coancestry, a difference probably mediated through distinct Irish and British demographic histories including even more marked genetic drift in Ireland.

This article uses isonymy to test predictions about the genetic structure of Irish populations made on the basis of geography and population history, and compares the mid-nineteenth century population of Ireland with the late nineteenth century Irish-born population resident in England and Wales. Surname data were derived from (1) the householders named in the index to Griffith's valuation of Ireland, a survey undertaken between 1846 and 1864, and (2) of Irish-born residents named in 1881 census of England and Wales. Visual representation of the Griffith's valuation isonymy matrix by multidimensional scaling (MDS) gives a result very close to the geographical distribution of Irish counties, and Mantel matrix correlation shows random isonymy between counties to be negatively associated with geographical distance, generally decaying according to a pattern of isolation-by-distance, with exceptions that can be explained in terms of Irish population history. Some 141,360 Irish-born residents in England and Wales at the 1881 census were assigned to an Irish county of origin, and random isonymy by county of birth for this group also shows a close correspondence to Irish geography. The Mantel matrix correlation between the Irish in Ireland and the Irish in England is 0.855, R(2)= 0.7306, indicating that the emigrant Irish in England were representative of the populations of the Irish counties from which they were derived. This result, together with the strong geographical patterning of surnames in Ireland, suggests that isonymy can be used to investigate the population structure and origin of Irish emigrant groups in Britain and potentially throughout the Irish diaspora. Am. J. Hum. Biol. 2009.(c) 2008 Wiley-Liss, Inc.

A previous study of Irish Y-chromosomes uncovered a likely patrilineal kinship basis to the most prominent early Irish tribal entity/kingdom, the Uí Néill, who dominated the North of the Island during the early medieval period (600-1,000 AD). However, it is unknown to what extent this was a general feature of the multitude of Irish kingdoms that existed over the same period. Irish surnames are patrilineally inherited in a similar manner to the Y-chromosome and their origin can often be traced to pre-existing tribal units. We genotyped 17 microsatellites in 247 Y-chromosomes from men with surnames that are purported to be derived from two different tribes (Eóganacht and Dál Cais) from the Southern province of Munster, as well as a third cohort of random names from the same geographic area. Although there is some sharing of Y-chromosomes between surnames of the same putative origin, there was no clear distinction between either grouping and the control, suggesting that the level of Uí Néill patrilineal kinship was not a universal feature of Irish tribal units. In turn this argues that an extensive extended clan or biological legacy of an eponymous founding ancestor was not necessarily a crucial factor in their establishment. Am J Phys Anthropol, 2008.(c) 2008 Wiley-Liss, Inc.

The genetic structures of past human populations are obscured by recent migrations and expansions, and can been observed only indirectly by inference from modern samples. However, the unique link between a heritable cultural marker, the patrilineal surname, and a genetic marker, the Y chromosome, provides a means to target sets of modern individuals that might resemble populations at the time of surname establishment. As a test case, we studied samples from the Wirral peninsula and West Lancashire, in northwest England. Place names and archaeology show clear evidence of a past Viking presence, but heavy immigration and population growth since the Industrial Revolution are likely to have weakened the genetic signal of a thousand-year-old Scandinavian contribution. Samples ascertained on the basis of two generations of residence were compared with independent samples based on known ancestry in the region, plus the possession of a surname known from historical records to have been present there in medieval times. The Y-chromosomal haplotypes of these two sets of samples are significantly different, and in admixture analyses the surname-ascertained samples show markedly greater Scandinavian ancestry proportions, supporting the idea that northwest England was once heavily populated by Scandinavian settlers. The method of historical surname-based ascertainment promises to allow investigation of the influence of migration and drift over the last few centuries in changing the population structure of Britain, and will have general utility in other regions where surnames are patrilineal and suitable historical records survive.

Objectives: Using Y chromosome short tandem repeat (YSTR) genotypes,(1) evaluate the accuracy and completeness of the Lancaster County Old Order Amish (OOA) genealogical records and (2) estimate YSTR mutation rates. Methods: Nine YSTR markers were genotyped in 739 Old Order Amish males who participated in several ongoing genetic studies of complex traits and could be connected into one of 28 all-male lineage pedigrees constructed using the Anabaptist Genealogy Database and the query software PedHunter. A putative founder YSTR haplotype was constructed for each pedigree, and observed and inferred father-son transmissions were used to estimate YSTR mutation rates. Results: We inferred 27 distinct founder Y chromosome haplotypes in the 28 male lineages, which encompassed 27 surnames accounting for 98% of Lancaster OOA households. Nearly all deviations from founder haplotypes were consistent with mutation events rather than errors. The estimated marker-specific mutation rates ranged from 0 to 1.09%(average 0.33% using up to 283 observed meioses only and 0.28% using up to 1,232 observed and inferred meioses combined). Conclusions: These data confirm the accuracy and completeness of the male lineage portion of the Anabaptist Genealogy Database and contribute mutation rate estimates for several commonly used Y chromosome STR markers. Copyright (c) 2007 S. Karger AG, Basel.

The polymorphism of the male-specific portion of the Y chromosome has been increasingly used to describe the composition of the European gene pool and to reconstruct its formation. Here the theoretical grounds and the limitations of this approach are presented, together with the different views on debated issues. The emerging picture for the composition of the male gene pool of the continent is illustrated, but local peculiarities that represent departures from the main trends are also highlighted, in order to illustrate the main unifying feature, i.e. the overlay of recent patterns onto more ancient ones. A synopsis of the main findings and conclusions obtained in regional studies has also been compiled.

The Vikings (or Norse) played a prominent role in Irish history but, despite this, their genetic legacy in Ireland, which may provide insights into the nature and scale of their immigration, is largely unexplored. Irish surnames, some of which are thought to have Norse roots, are paternally inherited in a similar manner to Y-chromosomes. The correspondence of Scandinavian patrilineal ancestry in a cohort of Irish men bearing surnames of putative Norse origin was examined using both slow mutating unique event polymorphisms and relatively rapidly changing short tandem repeat Y-chromosome markers. Irish and Scandinavian admixture proportions were explored for both systems using six different admixture estimators, allowing a parallel investigation of the impact of method and marker type in Y-chromosome admixture analysis. Admixture proportion estimates in the putative Norse surname group were highly consistent and detected little trace of Scandinavian ancestry. In addition, there is scant evidence of Scandinavian Y-chromosome introgression in a general Irish population sample. Although conclusions are largely dependent on the accurate identification of Norse surnames, the findings are consistent with a relatively small number of Norse settlers (and descendents) migrating to Ireland during the Viking period (ca. AD 800-1200) suggesting that Norse colonial settlements might have been largely composed of indigenous Irish. This observation adds to previous genetic studies that point to a flexible Viking settlement approach across North Atlantic Europe.European Journal of Human Genetics advance online publication, 6 September 2006; doi:10.1038/sj.ejhg.5201709.

ABSTRACT: BACKGROUND: The comparative analysis of genome sequences emerging for several avian species with the fully sequenced chicken genome enables the genome-wide investigation of selective processes in functionally important chicken genes. In particular, because of pathogenic challenges it is expected that genes involved in the chicken immune system are subject to particularly strong adaptive pressure. Signatures of selection detected by inter-species comparison may then be investigated at the population level in global chicken populations to highlight potentially relevant functional polymorphisms. RESULTS: Comparative evolutionary analysis of chicken (Gallus gallus) and zebra finch (Taeniopygia guttata) genes identified interleukin 4 receptor alpha-chain (IL-4Ralpha), a key cytokine receptor as a candidate with a significant excess of substitutions at nonsynonymous sites, suggestive of adaptive evolution. Resequencing and detailed population genetic analysis of this gene in diverse village chickens from Asia and Africa, commercial broilers, and in outgroup species red jungle fowl (JF), grey JF, Ceylon JF, green JF, grey francolin and bamboo partridge, suggested elevated and balanced diversity across all populations at this gene, acting to preserve different high-frequency alleles at two nonsynonymous sites. CONCLUSIONS: Haplotype networks indicate that red JF is the primary contributor of diversity at chicken IL-4Ralpha: the signature of variation observed here may be due to the effects of domestication, admixture and introgression, which produce high diversity. However, this gene is a key cytokine-binding receptor in the immune system, so balancing selection related to the host response to pathogens cannot be excluded.

There have been significant evolutionary pressures on the chicken during both its speciation and its subsequent domestication by man. Infectious diseases are expected to have exerted strong selective pressures during these processes. Consequently, it is likely that genes associated with disease susceptibility or resistance have been subject to some form of selection. Two genes involved in the immune response (interferon-gamma and interleukin 1-beta) were selected for sequencing in diverse chicken populations from Pakistan, Sri Lanka, Bangladesh, Kenya, Senegal, Burkina Faso and Botswana, as well as six outgroup samples (grey, green, red and Ceylon jungle fowl and grey francolin and bamboo partridge). Haplotype frequencies, tests of neutrality, summary statistics, coalescent simulations and phylogenetic analysis by maximum likelihood were used to determine the population genetic characteristics of the genes. Networks indicate that these chicken genes are most closely related to the red jungle fowl. Interferon-gamma had lower diversity and considerable coding sequence conservation, which is consistent with its function as a key inflammatory cytokine of the immune response. In contrast, the pleiotropic cytokine interleukin 1-beta had higher diversity and showed signals of balancing selection moderated by recombination, yielding high numbers of diverse alleles, possibly reflecting broader functionality and potential roles in more diseases in different environments.

ABSTRACT: BACKGROUND: The capacity of a species or population to respond to and survive novel infectious disease challenge is one of the most significant selective forces shaping genetic diversity and the period following animal domestication was likely one of the most important in terms of newly emerging diseases. Inter-specific genome-wide comparison has suggested that genes, including cluster of differentiation 2 (CD2), ADP-ribosyltransferase 4 (ART4), tyrosine kinase binding protein (TYROBP) and interleukins IL2, IL5, IL13, may have undergone positive selection during the evolution of the bovine lineage. Past adaptive change implies that more recent variation may have also been subject to selective forces. RESULTS: In this paper, we re-sequence each of these genes in cattle cohorts from Europe, Africa and Asia to investigate patterns of polymorphism at the population level. Patterns of diversity are higher within Bos indicus suggesting different demographic history to that of Bos taurus. Significant coding polymorphism was observed within each of the cell-surface receptors. In Particular, CD2 shows two divergent haplotypes defined by a series of six derived nonsynonymous substitutions that are significantly clustered on the extracellular surface of the protein and give significant values for Fay and Wu's H, strongly suggesting a recent adaptive history. In contrast, the signaling molecules (especially IL13) display outlying allele frequency spectra which are consistent with the effects of selection but display negligible coding polymorphism. CONCLUSIONS: We present evidence suggestive of recent adaptive history in bovine immune genes; implying some correspondence between intra- and inter-specific signals of selection. Interestingly, three signaling molecules show negligible nonsynonymous variation but show outlying test statistics in contrast to three receptors, where it is protein sequence diversity that suggests selective history.

A previous study of Irish Y-chromosomes uncovered a likely patrilineal kinship basis to the most prominent early Irish tribal entity/kingdom, the Uí Néill, who dominated the North of the Island during the early medieval period (600-1,000 AD). However, it is unknown to what extent this was a general feature of the multitude of Irish kingdoms that existed over the same period. Irish surnames are patrilineally inherited in a similar manner to the Y-chromosome and their origin can often be traced to pre-existing tribal units. We genotyped 17 microsatellites in 247 Y-chromosomes from men with surnames that are purported to be derived from two different tribes (Eóganacht and Dál Cais) from the Southern province of Munster, as well as a third cohort of random names from the same geographic area. Although there is some sharing of Y-chromosomes between surnames of the same putative origin, there was no clear distinction between either grouping and the control, suggesting that the level of Uí Néill patrilineal kinship was not a universal feature of Irish tribal units. In turn this argues that an extensive extended clan or biological legacy of an eponymous founding ancestor was not necessarily a crucial factor in their establishment. Am J Phys Anthropol, 2008.(c) 2008 Wiley-Liss, Inc.

A proper understanding of population genetic stratification--differences in individual ancestry within a population--is crucial in attempts to find genes for complex traits through association mapping. We report on genomewide typing of ~10,000 single-nucleotide polymorphisms in 297 individuals, to explore population structure in Europeans of known and unknown ancestry. The results reveal the presence of several significant axes of stratification, most prominently in a northern-southeastern trend, but also along an east-west axis. We also demonstrate the selection and application of EuroAIMs (European ancestry informative markers) for ancestry estimation and correction. The Coriell Caucasian and CEPH (Centre d'Etude du Polymorphisme Humain) Utah sample panels, often used as proxies for European populations, are found to reflect different subsets of the continent's ancestry.

Atlantic salmon are typically anadromous, spending the majority of their lifetime in oceans and returning to fresh water to breed. This diversity of environments likely results in strong selective forces shaping their genome. In this paper, we present the first genomics approach to detect positive selection operating on the Salmo salar (salmon) lineage, an important aquaculture species. We identify a panel of candidate genes that may have been subject to adaptive evolution in this species. In particular, we identify a robust signature of positive selection operating on the salmon CD3gammadelta gene, which encodes one of the protein chains essential for formation of the T-cell receptor complex and for T-cell activation. Furthermore, we identified the particular codon sites that have been subject to positive selection in fish and highlight two sites flanking an important N-glycosylation site in this molecule.

Human skin pigmentation shows a strong positive correlation with ultraviolet radiation (UVR) intensity, suggesting that variation in skin color is, at least partially, due to adaptation via natural selection. We investigated the evolution of pigmentation variation by testing for the presence of positive directional selection in six pigmentation genes using an empirical F(ST) approach, through an examination of global diversity patterns of these genes in the CEPH-Diversity Panel, and by exploring signatures of selection in data from the International HapMap project. Additionally, we demonstrated a role for MATP in determining normal skin pigmentation variation using admixture mapping methods. Taken together (with the results of previous admixture mapping studies), these results point to the importance of several genes in shaping the pigmentation phenotype and a complex evolutionary history involving strong selection. Polymorphisms in two genes, ASIP and OCA2, may play a shared role in shaping light and dark pigmentation across the globe while SLC24A5, MATP, and TYR have a predominant role in the evolution of light skin in Europeans but not in East Asians. These findings support a case for the recent convergent evolution of a lighter pigmentation phenotype in Europeans and East Asians.

Skin pigmentation varies substantially across human populations in a manner largely coincident with ultraviolet radiation intensity. This observation suggests that natural selection in response to sunlight is a major force in accounting for pigmentation variability. We review recent progress in identifying the genes controlling this variation with a particular focus on the trait's evolutionary past and the potential role of testing for signatures of selection in aiding the discovery of functionally important genes. We have analyzed SNP data from the International HapMap project in 77 pigmentation candidate genes for such signatures. On the basis of these results and other similar work, we provide a tentative three-population model (West Africa, East Asia and North Europe) of the evolutionary-genetic architecture of human pigmentation. These results suggest a complex evolutionary history, with selection acting on different gene targets at different times and places in the human past. Some candidate genes may have been selected in the ancestral human population, others in the 'out of Africa' proto European-Asian population, whereas most appear to have selectively evolved solely in either Europeans or East Asians separately despite the pigmentation similarities between these two populations. Selection signatures can provide important clues to aid gene discovery. However, these should be viewed as complements, rather than replacements of, functional studies including linkage and association analyses, which can directly refine our understanding of the trait.

The Caucasus region is a complex cultural and ethnic mosaic, comprising populations that speak Caucasian, Indo-European and Altaic languages. Isolated mountain villages (auls) in Dagestan still preserve high level of genetic and cultural diversity and have patriarchal societies with a long history of isolation. The aim of this study was to understand the genetic history of five Dagestan highland auls with distinct ethnic affiliation (Avars, Chechens-Akkins, Kubachians, Laks, Tabasarans) using markers on the male-specific region of the Y chromosome. The groups analyzed here are all Muslims but speak different languages all belonging to the Nakh-Dagestanian linguistic family. The results show that the Dagestan ethnic groups share a common Y-genetic background, with deep-rooted genealogies and rare alleles, dating back to an early phase in the post-glacial recolonization of Europe. Geography and stochastic factors, such as founder effect and long-term genetic drift, driven by the rigid structuring of societies in groups of patrilineal descent, most likely acted as mutually reinforcing key factors in determining the high degree of Y-genetic divergence among these ethnic groups.Journal of Human Genetics advance online publication, 13 November 2009; doi:10.1038/jhg.2009.94.

By direct sequencing of two Y chromosomes inherited from the same paternal ancestor, a landmark study has derived a good direct estimate for the rate of base substitution mutations on the human Y chromosome.

Heritable surnames are highly diverse cultural markers of coancestry in human populations. A patrilineal surname is inherited in the same way as the non-recombining region of the Y chromosome and there should, therefore, be a correlation between the two. Studies of Y haplotypes within surnames, mostly of the British Isles, reveal high levels of coancestry among surname cohorts and the influence of confounding factors, including multiple founders for names, non-paternities and genetic drift. Combining molecular genetics and surname analysis illuminates population structure and history, has potential applications in forensic studies and, in the form of 'genetic genealogy', is an area of rapidly growing interest for the public.

Since the beginning of the nineties the field of forensic Y chromosome analysis has been successfully developed to become commonplace in laboratories working in crime casework all over the world. The ability to identify male-specific DNA renders highly variable Y-chromosomal polymorphisms, the STR sequences, an invaluable addition to the standard panel of autosomal loci used in forensic genetics. The male-specificity makes the Y chromosome especially useful in cases of male/female cell admixture, namely in sexual assault cases. On the other hand, the haploidy and patrilineal inheritance complicates the interpretation of a Y-STR match, because male relatives share for several generations an identical Y-STR profile. Since paternal relatives tend to live in the geographic and cultural territory of their ancestors, the Y chromosome analysis has a potential to make inferences on the population of origin of a given DNA profile. This review addresses the fields of application of Y chromosome haplotyping, the interpretation of results, databasing efforts and population genetics aspects.

Y-STR analysis is a common tool in forensic case work. Lately it has also been popular in genealogical research to determine the male lineage. We present the investigation of members of a family with a pedigree dating back to the 14th century. The aim of the study was to genetically confirm the kinship established genealogically, a method that is mainly based on the fact that individuals of the male lineage carry the same family name. We investigated fifteen male individuals who were connected to approximately forty different branches of the family tree using the Powerplex Y kit (Promega) that allows the detection of eleven Y-STRs. Our study shows that there can be differences between genealogical and genetic pedigrees indicating the need for additional genetic analysis.

To study the genetic polymorphisms of Y-chromosome-specific STR loci in Chinese of different surnames, 9 Y-STR loci were amplified by single fluorescent multiplex PCR and the PCR products were detected by using ABI PrismTM 3100 DNA Sequencer. Samples were randomly-selected from male blood donors in ShenZhen. These individuals, who were otherwise unrelated, had the most common surnames among Chinese as their surnames, namely Li, Wang or Zhang. There were 139 subjects with surname Li, 118 with surname Wang and 119 with the surname Zhang. In the Li population, a total of 126 haplotypes was found and 118 of them were unique, with a haplotype diversity 0.9974. In the Wang population, a total of 105 haplotypes was found and 94 of them were unique, with a haplotype diversity of 0.9953. In the Zhang population, a total of 101 haplotypes was found and 88 of them were unique, with a haplotype diversity of 0.9964. Our results indicated that the genetic polymorphisms of Y-STR haplotypes at these 9 loci in unrelated male individuals with Chinese surnames of Li, Wang or Zhang are highly polymorphic and showed no significant differences with our previous data of haplotype polymorphisms in unrelated male individuals from the Chinese ethnic Han population.

Objectives: Using Y chromosome short tandem repeat (YSTR) genotypes,(1) evaluate the accuracy and completeness of the Lancaster County Old Order Amish (OOA) genealogical records and (2) estimate YSTR mutation rates. Methods: Nine YSTR markers were genotyped in 739 Old Order Amish males who participated in several ongoing genetic studies of complex traits and could be connected into one of 28 all-male lineage pedigrees constructed using the Anabaptist Genealogy Database and the query software PedHunter. A putative founder YSTR haplotype was constructed for each pedigree, and observed and inferred father-son transmissions were used to estimate YSTR mutation rates. Results: We inferred 27 distinct founder Y chromosome haplotypes in the 28 male lineages, which encompassed 27 surnames accounting for 98% of Lancaster OOA households. Nearly all deviations from founder haplotypes were consistent with mutation events rather than errors. The estimated marker-specific mutation rates ranged from 0 to 1.09%(average 0.33% using up to 283 observed meioses only and 0.28% using up to 1,232 observed and inferred meioses combined). Conclusions: These data confirm the accuracy and completeness of the male lineage portion of the Anabaptist Genealogy Database and contribute mutation rate estimates for several commonly used Y chromosome STR markers. Copyright (c) 2007 S. Karger AG, Basel.

OBJECTIVES: There is convergent evidence from adoption, family, geographical, immigrant, molecular genetic, twin and, most recently, surname studies of suicide for genetic contributions to suicide risk. Surnames carry information about genetic relatedness or distance and, in patrilineal surname systems, are a close substitute for Y-chromosome markers and haplotypes, since surname transmission is similar to the transmission of the nonrecombining part of the Y chromosome. This study investigated whether differences in regional suicide rates correspond to the genetic structure of the Austrian population. METHODS: Differences in district-level standardized suicide rates 1988-94 between the five major surname regions identified for Austria were analyzed. The surname regions used in the analysis reflect the contemporary population structure and closely follow the natural borders found in the topography of Austria, less so its administrative division into nine states. RESULTS: Surname region accounted for a significant (P < 0.001) and substantial (38%) portion of the variance in district-level suicide rates. Adjusting the suicide rates for a set of five social and economic indicators that are established ecological correlates of suicide prevalence (income, and rates of the divorced, unemployed, elderly and Roman Catholics) left the results essentially unchanged. CONCLUSIONS: Regional differences in suicide rates within Austria correspond to the genetic structure of the population. The present evidence adds to related findings from geographical and surname studies of suicide that suggest a role for genetic risk factors for suicidal behavior. Genetic differences between subpopulations may partially account for the geography of suicide. Study limitations and directions for future research are discussed.

We have characterized the Y chromosome carried by President Thomas Jefferson, the general rarity of which supported the idea that he, or a patrilineal relative, fathered the last son of his slave Sally Hemings. It belongs to haplogroup K2, a lineage representing only approximately 1% of chromosomes worldwide, and most common in East Africa and the Middle East. Phylogenetic network analysis of its Y-STR (short tandem repeat) haplotype shows that it is most closely related to an Egyptian K2 haplotype, but the presence of scattered and diverse European haplotypes within the network is nonetheless consistent with Jefferson's patrilineage belonging to an ancient and rare indigenous European type. This is supported by the observation that two of 85 unrelated British men sharing the surname Jefferson also share the President's Y-STR haplotype within haplogroup K2. Our findings represent a cautionary tale in showing the difficulty of assigning individual ancestry based on a Y-chromosome haplotype, particularly for rare lineages where population data are scarce. Am J Phys Anthropol, 2007.(c) 2007 Wiley-Liss, Inc.